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Yorodumi- PDB-1oiq: Imidazopyridines: a potent and selective class of Cyclin-dependen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oiq | ||||||
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Title | Imidazopyridines: a potent and selective class of Cyclin-dependent Kinase inhibitors identified through Structure-based hybridisation | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | KINASE / PROTEIN KINASE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / MITOSIS / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Beattie, J.F. / Breault, G.A. / Byth, K.F. / Culshaw, J.D. / Ellston, R.P.A. / Green, S. / Minshull, C.A. / Norman, R.A. / Pauptit, R.A. / Thomas, A.P. / Jewsbury, P.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: Imidazo[1,2-A]Pyridines: A Potent and Selective Class of Cyclin-Dependent Kinase Inhibitors Identified Through Structure-Based Hybridisation Authors: Anderson, M. / Beattie, J.F. / Breault, G.A. / Breed, J. / Byth, K.F. / Culshaw, J.D. / Ellston, R.P.A. / Green, S. / Minshull, C.A. / Norman, R.A. / Pauptit, R.A. / Stanway, J. / Thomas, A.P. / Jewsbury, P.J. #1: Journal: J.Med.Chem. / Year: 1996 Title: High-Resolution Crystal Structures of Human Cyclin-Dependent Kinase 2 with and without ATP: Bound Waters and Natural Ligand as a Guide for Inhibitor Design Authors: Schulze-Gahmen, U. / De Bondt, H. / Kim, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oiq.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oiq.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1oiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oiq_validation.pdf.gz | 732.4 KB | Display | wwPDB validaton report |
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Full document | 1oiq_full_validation.pdf.gz | 735.3 KB | Display | |
Data in XML | 1oiq_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1oiq_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oiq ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oiq | HTTPS FTP |
-Related structure data
Related structure data | 1oirC 1oitC 1h0u C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34002.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-HDU / |
#3: Water | ChemComp-HOH / |
Compound details | FUNCTION: PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE. INTERACTS WITH CYCLINS A, D, OR E. ...FUNCTION: PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE. INTERACTS WITH CYCLINS A, D, OR E. ACTIVITY OF CDK2 IS MAXIMAL DURING S PHASE AND G2. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN AT 10MG/ML WELL BUFFER CONTAINING 17.5% PEG3350, 200MM HEPES, PH7.0, 100MM AMMONIUM ACETATE, pH 7.00 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop / Details: Lawrie, A.M., (1997) Nature Struct. Biol., 4, 796. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.875 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.875 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→43.85 Å / Num. obs: 12637 / % possible obs: 93.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.31→2.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.2 / % possible all: 83 |
Reflection | *PLUS Highest resolution: 2.31 Å / Num. measured all: 60244 / Rmerge(I) obs: 0.132 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→43.85 Å / SU B: 8.315 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.282 / Details: TLS REFINEMENT DONE
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Displacement parameters | Biso mean: 29.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→43.85 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.233 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |